13-112182341-C-T

Variant names:

• chr13-112182341-C-T
• rs9324268
• XR_944282.1:n.1487G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_944282.1(LOC105370370):​n.1487G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 152,010 control chromosomes in the GnomAD database, including 5,726 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.26 (5726 hom., cov: 33)
• Consequence: LOC105370370 XR_944282.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.818
• Publications: 6 publications found

Genes affected

LOC105370370 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.472 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370370	XR_944282.1	n.1487G>A		non_coding_transcript_exon_variant	Exon 4 of 6
LOC105370370	XR_944284.1	n.1127G>A		non_coding_transcript_exon_variant	Exon 3 of 5
LOC105370370	XR_944285.1	n.1487G>A		non_coding_transcript_exon_variant	Exon 4 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000306489	ENST00000819056.1	n.785+446G>A		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.258 AC: 39173 AN: 151892 Hom.: 5715 Cov.: 33

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.188

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.225

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.258 AC: 39218 AN: 152010 Hom.: 5726 Cov.: 33 AF XY: 0.261 AC XY: 19401 AN XY: 74306

African (AFR) AF: 0.369 AC: 15286 AN: 41442

American (AMR) AF: 0.237 AC: 3625 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 560 AN: 3470

East Asian (EAS) AF: 0.488 AC: 2505 AN: 5132

South Asian (SAS) AF: 0.284 AC: 1371 AN: 4824

European-Finnish (FIN) AF: 0.185 AC: 1961 AN: 10580

Middle Eastern (MID) AF: 0.182 AC: 53 AN: 292

European-Non Finnish (NFE) AF: 0.194 AC: 13185 AN: 67966

Other (OTH) AF: 0.233 AC: 492 AN: 2112

Alfa AF: 0.213 Hom.: 16401

Bravo AF: 0.263

Asia WGS AF: 0.392 AC: 1361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.1
DANN	Benign	0.42
PhyloP100		-0.82

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs9324268; hg19: chr13-112836655;